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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...aatgtttgagagtaggaagtttacctgaaaatgcatatattaattctgaatgattccatcgaaaccttcgagtatgctgatttctagttctacgttgcagATAATGCACAGATGTTGCCTCGACTGGATCCTCCTCAGGAACTGAAGTTGAAGCAGCTGACTGTAATGACTTTGGCAGAAACAGCCAAG

Basic information

species Physcomitrella patens
transcript PP1S271_80V6.1
intron # 2
splice site 3'
intron type U2

Mapped EST sequences

Showing partial alignments of ESTs and genomic sequences. See full alignments


 ATGC     EST sequence
 ATGC     genomic sequence (exon)
 ATGC     genomic sequence (truncated intron)


EST: gi|100417583|gb|BY975553.1|BY975553
EST:     TTTAGATCTGCTTCGACTCTTTGCTCATGGGACCTGGACCGATTACAAAA                         ATA-TGCACAGATTTTGCCTCGACTGAATCCTCCTCAGGAACTGAAGTTGA
genomic: TTTAGATCTGCTTCGACTCTTTGCTCATGGGACCTGGACCGATTACAAAAgtaagtgttc ... tacgttgcagATAATGCACAGATGTTGCCTCGACTGGATCCTCCTCAGGAACTGAAGTTGA
EST: gi|162245043|gb|FC421569.1|FC421569
EST:     TTTAGATCTGCTTCGACTCTTTGCTCATGGGACCTGGACCGATTACAAAA                         ATAATGCACAGATGTTGCCTCGACTGGATCCTCCTCAGGAACTGAAGTTGA
genomic: TTTAGATCTGCTTCGACTCTTTGCTCATGGGACCTGGACCGATTACAAAAgtaagtgttc ... tacgttgcagATAATGCACAGATGTTGCCTCGACTGGATCCTCCTCAGGAACTGAAGTTGA
EST: gi|208357665|gb|DC934117.1|DC934117
EST:     TTTAGATCTGCTTCGACTCTTTGCTCATGGGACCTGGACCGATTACAAAA                         ATAATGCACAGATGTTGCCTCGACTGGATCCTCCTCAGGAACTGAAGTTGA
genomic: TTTAGATCTGCTTCGACTCTTTGCTCATGGGACCTGGACCGATTACAAAAgtaagtgttc ... tacgttgcagATAATGCACAGATGTTGCCTCGACTGGATCCTCCTCAGGAACTGAAGTTGA
EST: gi|18330929|gb|BJ162935.1|BJ162935
EST:     TTTAGATCTGCTTCGACTCTTTGCTCATGGGACCTGGACCGATTACAAAA                         ATAATGCACAGATGTTGCCTCGACTGGATCCTCCTCAGGAACTGAAGTTGA
genomic: TTTAGATCTGCTTCGACTCTTTGCTCATGGGACCTGGACCGATTACAAAAgtaagtgttc ... tacgttgcagATAATGCACAGATGTTGCCTCGACTGGATCCTCCTCAGGAACTGAAGTTGA
EST: gi|18368238|gb|BJ200323.1|BJ200323
EST:     TTTAGATCTGCTTCGACTCTTTGCTCATGGGACCTGGACCGATTACAAAA                         ATAATGCACAGATGTTGCCTCGACTGGATCCTCCTCAGGAACTGAAGTTGA
genomic: TTTAGATCTGCTTCGACTCTTTGCTCATGGGACCTGGACCGATTACAAAAgtaagtgttc ... tacgttgcagATAATGCACAGATGTTGCCTCGACTGGATCCTCCTCAGGAACTGAAGTTGA
EST: gi|18350728|gb|BJ182779.1|BJ182779
EST:     TTTAGATCTGCTTCGACTCTTTGCTCATGGGACCTGGACCGATTACAAAA                         ATAATGCACAGATGTTGCCTCGACTGGATCCTCCTCAGGAACTGAAGTTGA
genomic: TTTAGATCTGCTTCGACTCTTTGCTCATGGGACCTGGACCGATTACAAAAgtaagtgttc ... tacgttgcagATAATGCACAGATGTTGCCTCGACTGGATCCTCCTCAGGAACTGAAGTTGA
EST: gi|100452982|gb|CJ975541.1|CJ975541
EST:     TTTAGATCTGCTTCGACTCTTTGCTCATGGGACCTGGACCGATTACAAAA                         ATAATGCACAGATGTTGCCTCGACTGGATCCTCCTCAGGAACTGAAGTTGA
genomic: TTTAGATCTGCTTCGACTCTTTGCTCATGGGACCTGGACCGATTACAAAAgtaagtgttc ... tacgttgcagATAATGCACAGATGTTGCCTCGACTGGATCCTCCTCAGGAACTGAAGTTGA
EST: gi|162245042|gb|FC421568.1|FC421568
EST:     CCGATTACAAAA                         ATAATGCACAGATGTTGCCTCGACTGGATCCTCCTCAGGAACTGAAGTTGA
genomic: CCGATTACAAAAgtaagtgttc ... tacgttgcagATAATGCACAGATGTTGCCTCGACTGGATCCTCCTCAGGAACTGAAGTTGA
EST: gi|162266011|gb|FC442696.1|FC442696
EST:     TTTAGATCTGCTTCGACTCTTTGCTCATGGGACCTGGACCGATTACAAAA                         ATAATGCACAGATGTTGCCTCGACTGGATCCTCCTCAGGAACTGAAGTTGA
genomic: TTTAGATCTGCTTCGACTCTTTGCTCATGGGACCTGGACCGATTACAAAAgtaagtgttc ... tacgttgcagATAATGCACAGATGTTGCCTCGACTGGATCCTCCTCAGGAACTGAAGTTGA
EST: gi|208352193|gb|DC901714.1|DC901714
EST:     TTTAGATCTGCTTCGACTCTTTGCTCATGGGACCTGGACCGATTACAAAA                         ATAATGCACAGATGTTGCCTCGACTGGATCCTCCTCAGGAACTGAAGTTGA
genomic: TTTAGATCTGCTTCGACTCTTTGCTCATGGGACCTGGACCGATTACAAAAgtaagtgttc ... tacgttgcagATAATGCACAGATGTTGCCTCGACTGGATCCTCCTCAGGAACTGAAGTTGA
EST: gi|162183315|gb|FC359230.1|FC359230
EST:     TTTAGATCTGCTTCGACTCTTTGCTCATGGGACCTGGACCGATTACAAAA                         ATAATGCACAGATGTTGCCTCGACTGGATCCTCCTCAGGAACTGAAGTTGA
genomic: TTTAGATCTGCTTCGACTCTTTGCTCATGGGACCTGGACCGATTACAAAAgtaagtgttc ... tacgttgcagATAATGCACAGATGTTGCCTCGACTGGATCCTCCTCAGGAACTGAAGTTGA
EST: gi|100439177|gb|BY980132.1|BY980132
EST:     TTTAGATCTGCTTCGACTCTTTGCTCATGGGACCCGGACCGATTACAAAA                         ATAATGCACAGATGTTGCCTCGACTGGATCCTCCTCAGGAACTGAAGTTGA
genomic: TTTAGATCTGCTTCGACTCTTTGCTCATGGGACCTGGACCGATTACAAAAgtaagtgttc ... tacgttgcagATAATGCACAGATGTTGCCTCGACTGGATCCTCCTCAGGAACTGAAGTTGA
EST: gi|162204856|gb|FC381187.1|FC381187
EST:     TTTAGATCTGCTTCGACTCTTTGCTCATGGGACCTGGACCGATTACAAAA                         ATAATGCACAGATGTTGCCTCGACTGGATCCTCCTCAGGAACTGAAGTTGA
genomic: TTTAGATCTGCTTCGACTCTTTGCTCATGGGACCTGGACCGATTACAAAAgtaagtgttc ... tacgttgcagATAATGCACAGATGTTGCCTCGACTGGATCCTCCTCAGGAACTGAAGTTGA
EST: gi|22492731|gb|BU052654.1|BU052654
EST:     TTTAGATCTGCTTCGACTCTTTGCTCATGGGACCTGGACCGATTACAAAA                         ATAATGCACAGATGTTGCCTCGACTGGATCCTCCTCAGGAACTGAAGTTGA
genomic: TTTAGATCTGCTTCGACTCTTTGCTCATGGGACCTGGACCGATTACAAAAgtaagtgttc ... tacgttgcagATAATGCACAGATGTTGCCTCGACTGGATCCTCCTCAGGAACTGAAGTTGA

RNA-Seq data


 ATGC   Supported by RNA-Seq exonic block that spans over the splice site

 atgs   Truncated intron sequence

Each block is as long as the maximal overhang of any read spanning the junction.
The score is the number of alignments spanning the junction.


Found data for 1 RNA-Seqlibrary.


Block sizes: 10 (upstream exon), 34 (downstream exon)
Score: 4

TTAAAAGGAACGGAGCATTCTGCATCTTTAGATCTGCTTCGACTCTTTGCTCATGGGACCTGGACCGATTACAAAAgtaagtgttc ... tacgttgcagATAATGCACAGATGTTGCCTCGACTGGATCCTCCTCAGGAACTGAAGTTGAAGCAGCTGACTGTAATGACTTTGGCAGAAACAGCCAAG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ctgaatgattccatcgaaaccttcgagtatgctgatttctagttctacgttgcagATAATGCACAGATGTTGCCTCGACTGGATCCTCCTCAGGAACTGAAGTTGAAGCAGCTGACTGTAATGACTTTGGCAGAAACAGCCAAG
                             tgctgat  putative branch site (score: 4)
                                  atttcta  TA-rich tract
















Putative cis-regulatory sequences

 atgc intron ATGC exonic elements by Pertea et al.
 ATGC exon atgc putative intronic elements
 ATGC putative exonic elements identified for retained introns
        10        20        30        40        50        60        70        80        90        100       110       120       130       140       150       160       170       180       190       200       210       220 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
aatgtttgagagtaggaagtttacctgaaaatgcatatattaattctgaatgattccatcgaaaccttcgagtatgctgatttctagttctacgttgcagATAATGCACAGATGTTGCCTCGACTGGATCCTCCTCAGGAACTGAAGTTGAAGCAGCTGACTGTAATGACTTTGGCAGAAACAGCCAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTGA